Contacts of the strand formed by residues 291 - 294 (chain C) in PDB entry 4OIN


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with ALA 291 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200C  LEU*     4.0    20.0    -      -       +      -
    261C  ILE*     3.5    21.2    -      -       +      +
    262C  ALA*     3.3    14.5    -      -       +      +
    289C  THR*     2.6    27.4    +      -       -      -
    290C  LEU*     1.3    82.9    -      -       -      +
    292C  ARG*     1.3    68.6    +      -       -      +
    298C  PHE*     5.5     2.2    -      -       +      -
    299C  LYS      3.3    15.9    -      -       -      +
    300C  ASP*     4.3     1.1    -      -       -      +
    301C  GLU*     3.8     4.7    -      -       -      -
    303C  PHE*     5.4     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 292 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    262C  ALA*     3.8     9.2    -      -       -      -
    286C  SER*     3.9    24.4    +      -       -      -
    287C  GLY*     5.3     3.8    -      -       -      +
    289C  THR*     4.7     3.1    -      -       -      +
    291C  ALA*     1.3    79.9    -      -       -      +
    293C  PHE*     1.3    64.4    +      -       -      +
    294C  GLU*     3.5    29.7    +      -       +      +
    298C  PHE*     3.2    10.2    -      -       -      +
    299C  LYS*     2.9    58.4    +      -       +      +
    300C  ASP      5.2     3.0    +      -       -      -
    301C  GLU*     3.3    27.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 293 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    250C  ARG*     5.9     4.0    -      -       -      -
    254C  VAL*     3.9    25.8    -      -       +      -
    258C  TYR*     3.6    28.8    -      +       +      -
    262C  ALA*     4.1     2.8    -      -       -      +
    292C  ARG*     1.3    74.6    -      -       -      +
    294C  GLU*     1.3    60.4    +      -       -      +
    295C  ASP      5.2     0.7    -      -       -      -
    296C  GLY*     3.2    43.3    -      -       -      -
    297C  GLU*     3.4     6.5    -      -       -      -
    298C  PHE*     3.5    26.7    -      +       +      -
----------------------------------------------------------
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Residues in contact with GLU 294 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    292C  ARG*     3.5    41.5    +      -       +      -
    293C  PHE*     1.3    75.6    -      -       -      +
    295C  ASP*     1.3    91.1    +      -       -      +
    296C  GLY      3.1     2.2    +      -       -      -
    297C  GLU*     2.8    28.7    +      -       -      +
    299C  LYS*     5.3    12.6    -      -       +      +
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il